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B1KQD0

- DAPF_SHEWM

UniProt

B1KQD0 - DAPF_SHEWM

Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Shewanella woodyi (strain ATCC 51908 / MS32)
Status
Reviewed - Annotation score: 3 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 49 (01 Oct 2014)
      Sequence version 1 (29 Apr 2008)
      Previous versions | rss
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    Functioni

    Catalyzes the stereoinversion of LL-2,6-diaminoheptanedioate (L,L-DAP) to meso-diaminoheptanedioate (meso-DAP), a precursor of L-lysine and an essential component of the bacterial peptidoglycan.UniRule annotation

    Catalytic activityi

    LL-2,6-diaminoheptanedioate = meso-diaminoheptanedioate.UniRule annotation

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei12 – 121SubstrateUniRule annotation
    Binding sitei45 – 451SubstrateUniRule annotation
    Binding sitei65 – 651SubstrateUniRule annotation
    Active sitei74 – 741Proton donor/acceptorUniRule annotation
    Binding sitei162 – 1621SubstrateUniRule annotation
    Sitei164 – 1641Important for catalytic activityUniRule annotation
    Binding sitei195 – 1951SubstrateUniRule annotation
    Sitei213 – 2131Important for catalytic activityUniRule annotation
    Active sitei222 – 2221Proton donor/acceptorUniRule annotation

    GO - Molecular functioni

    1. diaminopimelate epimerase activity Source: UniProtKB-HAMAP

    GO - Biological processi

    1. lysine biosynthetic process via diaminopimelate Source: UniProtKB-HAMAP

    Keywords - Molecular functioni

    Isomerase

    Keywords - Biological processi

    Amino-acid biosynthesis, Lysine biosynthesis

    Enzyme and pathway databases

    BioCyciSWOO392500:GI2C-504-MONOMER.
    UniPathwayiUPA00034; UER00025.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Diaminopimelate epimeraseUniRule annotation (EC:5.1.1.7UniRule annotation)
    Short name:
    DAP epimeraseUniRule annotation
    Gene namesi
    Name:dapFUniRule annotation
    Ordered Locus Names:Swoo_0487
    OrganismiShewanella woodyi (strain ATCC 51908 / MS32)
    Taxonomic identifieri392500 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaAlteromonadalesShewanellaceaeShewanella
    ProteomesiUP000002168: Chromosome

    Subcellular locationi

    Cytoplasm UniRule annotation

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 279279Diaminopimelate epimerasePRO_1000099267Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Disulfide bondi74 ↔ 222

    Keywords - PTMi

    Disulfide bond

    Interactioni

    Protein-protein interaction databases

    STRINGi392500.Swoo_0487.

    Structurei

    3D structure databases

    ProteinModelPortaliB1KQD0.
    SMRiB1KQD0. Positions 2-277.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni9 – 102Substrate bindingUniRule annotation
    Regioni74 – 763Substrate bindingUniRule annotation
    Regioni213 – 2142Substrate bindingUniRule annotation
    Regioni223 – 2242Substrate bindingUniRule annotation

    Sequence similaritiesi

    Belongs to the diaminopimelate epimerase family.UniRule annotation

    Phylogenomic databases

    eggNOGiCOG0253.
    HOGENOMiHOG000220466.
    KOiK01778.
    OMAiLIVEPPY.
    OrthoDBiEOG6ND0M5.

    Family and domain databases

    HAMAPiMF_00197. DAP_epimerase.
    InterProiIPR018510. DAP_epimerase_AS.
    IPR001653. DAP_epimerase_DapF.
    [Graphical view]
    PANTHERiPTHR31689. PTHR31689. 1 hit.
    PfamiPF01678. DAP_epimerase. 2 hits.
    [Graphical view]
    TIGRFAMsiTIGR00652. DapF. 1 hit.
    PROSITEiPS01326. DAP_EPIMERASE. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    B1KQD0-1 [UniParc]FASTAAdd to Basket

    « Hide

    MIHFAKMHGL GNDFMVVDGV TQNVFFSPEQ IKRLADRNFG VGFDQLLLVE    50
    PPYDPDLDFH YRIFNADGGE VEQCGNGARC FARFVRNKGL TNKHKIKVST 100
    SNGKITLRLE RDGNVTVNMG VPVLDPSKIP FNAKRVEKTY LLQTSSSHAM 150
    ETFLCGAISM GNPHCVLEVE DIEHAEVERI GALLTQNERF PKGVNVGFMQ 200
    VIDAGHIKLR VYERGAAETL ACGTGACAAA AVGQLQGKLN KMVRVDLPGG 250
    TLTINWEGEG NPLWMTGPAE HVYDGQIPQ 279
    Length:279
    Mass (Da):30,626
    Last modified:April 29, 2008 - v1
    Checksum:i2D865DEF34E6E969
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP000961 Genomic DNA. Translation: ACA84785.1.
    RefSeqiWP_012323134.1. NC_010506.1.
    YP_001758880.1. NC_010506.1.

    Genome annotation databases

    EnsemblBacteriaiACA84785; ACA84785; Swoo_0487.
    GeneIDi6114721.
    KEGGiswd:Swoo_0487.
    PATRICi23603223. VBISheWoo126588_0508.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP000961 Genomic DNA. Translation: ACA84785.1 .
    RefSeqi WP_012323134.1. NC_010506.1.
    YP_001758880.1. NC_010506.1.

    3D structure databases

    ProteinModelPortali B1KQD0.
    SMRi B1KQD0. Positions 2-277.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 392500.Swoo_0487.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai ACA84785 ; ACA84785 ; Swoo_0487 .
    GeneIDi 6114721.
    KEGGi swd:Swoo_0487.
    PATRICi 23603223. VBISheWoo126588_0508.

    Phylogenomic databases

    eggNOGi COG0253.
    HOGENOMi HOG000220466.
    KOi K01778.
    OMAi LIVEPPY.
    OrthoDBi EOG6ND0M5.

    Enzyme and pathway databases

    UniPathwayi UPA00034 ; UER00025 .
    BioCyci SWOO392500:GI2C-504-MONOMER.

    Family and domain databases

    HAMAPi MF_00197. DAP_epimerase.
    InterProi IPR018510. DAP_epimerase_AS.
    IPR001653. DAP_epimerase_DapF.
    [Graphical view ]
    PANTHERi PTHR31689. PTHR31689. 1 hit.
    Pfami PF01678. DAP_epimerase. 2 hits.
    [Graphical view ]
    TIGRFAMsi TIGR00652. DapF. 1 hit.
    PROSITEi PS01326. DAP_EPIMERASE. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 51908 / MS32.

    Entry informationi

    Entry nameiDAPF_SHEWM
    AccessioniPrimary (citable) accession number: B1KQD0
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: March 24, 2009
    Last sequence update: April 29, 2008
    Last modified: October 1, 2014
    This is version 49 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3